support output from cwltool's `--pack`

[mr-c]

Example: https://view.commonwl.org/workflows/github.com/ProteinsWebTeam/ebi-metagenomics-cwl/tree/packed/workflows/emg-pipeline-v3-packed.cwl

Or in other words, support visualizing subworkflows in situ

[hmenager]

+1 that would be really helpful!

[MarkRobbo]

Support for subworkflows has improved in v1.1.0 due to cwltool support.

It is now a lot easier for us to implement visualisation of subworkflows in their own clusters in-place if the workflow is packed.

[mr-c]

@MarkRobbo Or worse case, you can --pack it for the user?

[MarkRobbo]

@mr-c The problem is with the workflows being packed rather than the opposite.

It is then difficult to give each page a unique URL as # cannot be used due to those parameters not being passed to the server.

Currently the application assumes one URL refers to one cwl file, which is not the case with packed workflows. Though there is room for support in the code if we can come up with a strategy for the URLs.

[mr-c]

@MarkRobbo Why not URL encode the hash as %23?

[MarkRobbo]

@mr-c that's possible and would work in the normal application flow, but users manually typing # into the browser to navigate to different subworkflows would not have it URL encoded which could make that confusing.

Edit: I've also done some quick testing on this with some weird behaviour on the part of the browsers - not sure if this would work as an approach

[mr-c]

Can't you detect the presence of an unescaped hash and convert appropriately if it's a valid sub document?

[MarkRobbo]

@mr-c The only way to read them would be on the client side - I suppose it may be possible having loaded the page to redirect you to the escaped hash page using Javascript, but that is a little messy and there's no way to check if it actually exists at that point without an AJAX call.

As they are used for anchors etc, that information is not sent to the server at all.

[mr-c]

It is your call -- I think some messy code is often worth a better user experience.

[alexiswl]

I'm having issues with this.

If I try the following link I get:

https://view.commonwl.org/?url=https://github.com/umccr/cwl-ica/blob/main/.dockstore/dragen-somatic-with-germline-pipeline/4.2.4/dragen-somatic-with-germline-pipeline__4.2.4.packed.cwl.json

Error: No workflow files were found in the given directory

[mr-c]

I'm having issues with this.

If I try the following link I get:

https://view.commonwl.org/?url=https://github.com/umccr/cwl-ica/blob/main/.dockstore/dragen-somatic-with-germline-pipeline/4.2.4/dragen-somatic-with-germline-pipeline__4.2.4.packed.cwl.json

Error: No workflow files were found in the given directory

Can you try from a branch where the file extension is .cwl?

[alexiswl]

Same issue - https://view.commonwl.org/?url=https://github.com/umccr/cwl-ica/blob/test/no-extension-cwl-viewer/.dockstore/dragen-somatic-with-germline-pipeline/4.2.4/dragen-somatic-with-germline-pipeline__4.2.4.packed.json.cwl#